Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=f23c1b76d378fec01f1c1ee5de8fc08b10edc403;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=0795189676bc7b73ce0f7f0e95044a15164ae7e3;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 0795189..f23c1b7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,11 +1,27 @@ + Alignment Window Menus

Alignment Window Menus

File
- Fetch Sequence
  @@ -194,6 +210,12 @@
- Undefine Groups (Control U)
  The alignment will be reset with no defined groups.
  WARNING: This cannot be undone.
- Make Groups
  + The currently selected groups of the alignment will be + subdivided according to the contents of the currently selected region. +
  Use this to subdivide an alignment based on the + different combinations of residues observed at specific + positions. (new in jalview 2.5)
View @@ -206,22 +228,58 @@
Gather Views (G)
Each view associated with the alignment will be displayed within its own tab on the current alignment window.
Show→(all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
Hide→(all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
Show→(all Columns / Sequences / Sequences and Columns)
+ All hidden Columns / Sequences / Sequences and Columns will be revealed.
Hide→(all Columns / Sequences / Selected Region / All but Selected Region )
+ Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.
Automatic Scrolling
+ When selected, the view will automatically scroll to display the + highlighted sequence position corresponding to the position under the mouse + pointer in a linked alignment or structure view. +
Show Annotations
If this is selected the "Annotation Panel" will be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
Show Sequence Features
+
Autocalculated Annotation
Settings for the display of autocalculated annotation. +
- + Apply to all groups
  + When ticked, any modification to the current settings will be applied to all autocalculated annotation. +
- + Show Consensus Histogram
  + Enable or disable the display of the histogram above the consensus sequence. +
- + Show Consensus Profile
  + Enable or disable the display of the sequence logo above the consensus sequence. +
- + Group Conservation
  + When ticked, display a conservation row for all groups (only available for protein alignments). +
- + Apply to all groups
  + When ticked, display a consensus row for all groups. +
+
Show Sequence Features
Show or hide sequence features on this alignment.
Seqence Feature Settings...
Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and retrieve features from DAS annotation servers.

+
Sequence ID Tooltip (application only) +
This submenu's options allow the inclusion or exclusion of + non-positional sequence features or database cross references + from the tooltip shown when the mouse hovers over the sequence ID panel.
+
Alignment Properties...
+ Displays some simple statistics computed for the + current alignment view and any named properties defined on the + whole alignment.

Overview Window
A scaled version of the alignment will be displayed in a @@ -251,7 +309,6 @@
Scale Right
Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.
-
Show Sequence Limits
If this box is selected the sequence name will have the start and end position of the sequence appended to the name, in the format @@ -282,8 +339,14 @@ will appear as blank spaces.
You may set the default gap character in preferences.
+
Centre Annotation Labels
+ Select this to center labels along an annotation row + relative to their associated column (default is off, i.e. left-justified).
+
Show Unconserved
+ When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. +
+

Colour

Apply Colour To All Groups
@@ -333,7 +396,10 @@
by ID
This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
-
by Group
+
by Length
+ This will sort the sequences according to their length (excluding gap characters). If the sort is + repeated, the order of the sorted sequences will be inverted.
+
by Group
This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
@@ -368,6 +434,11 @@ BLOSUM62 scores in the alignment. See Principal Component Analysis.

+
Extract Scores ... (optional)
+ This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
+ When selected, these numbers are parsed into sequence associated annotation which can + then be used to sort the alignment via the Sort by→Score menu.
+

Autocalculate Consensus
For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the @@ -376,7 +447,15 @@

Web Service
- Selecting one of the following menu items starts a remote + +
Fetch DB References
+ This will use any of the database services that Jalview is aware + of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI) + to verify the sequence and retrieve all database cross references and PDB ids + associated with all or just the selected sequences in the alignment.
+
+
+ Selecting one of the following menu items starts a remote service on compute facilities at the University of Dundee. You need a continuous network connection in order to use these services through Jalview.